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1 Answer
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A lot of the matrix is what you would expect from reading the basic fluff. Guard working with the other imperial factions and with a few of the others to represent renegades. Tyranids can't ally with anyone because they would just eat them. Tau will work with anybody if it will advance the greater good. There's been some talk of the Emperor giving instructions to certain Marine legions to protect a certain alien race(hence the Marines and Tau being battle brothers). And the Eldar/Dark Eldar works a little better if you consider one part of the pair to be Eldar Corsairs instead of true Craftworld or Commorragh Eldar.

The fluff is in a state of flux right now. The Matt Ward authored codexes have done a number on established cannon. This is behind some of the weirder combinations you see in the matrix.

I think game balance was secondary to fluff when deciding who gets to ally with whom. Otherwise the Tyranids would have at least one ally option.

But the Tau/Eldar? I dunno, what other pairings in there don't make sense?
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PureferretSep 24 '12 at 13:56

@Pureferret Tau and Eldar are the two "good guy" alien races, so I think it makes sense that they would ally. Plus both those codexes are on deck for 2013 releases. That may shed more light on their partnership. But Necron/Orks is another weird combination.
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CaulynDarrSep 24 '12 at 14:53

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The 'nids not being able to ally with ANYONE is kind of dumb, anyone remember Genestealer Cults?
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aslumSep 24 '12 at 15:21

@CaulynDarr I've just read the Tau Codex, and the only mention of them is that the Tau destroyed a craftworld once and they've been at arms with each other since....hardly allies!
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PureferretApr 11 '13 at 12:20